Author: Lars S Jermiin; Renee A Catullo; Barbara R Holland
Title: A new phylogenetic protocol: Dealing with model misspecification and confirmation bias in molecular phylogenetics Document date: 2018_8_27
ID: hr6wfx4g_13
Snippet: Having inferred the phylogeny using model-based phylogenetic methods, it is possible to test the fit between tree, model and data (step 10 of the new protocol). A suitable test of goodness-of fit was proposed in 1993 (172) (Fig. 4) . In brief, using the inferred optimal tree, including the edge lengths, it is possible to simulate data sets under the null model (i.e., the inferred optimal model of sequence evolution with its parameter values inclu.....
Document: Having inferred the phylogeny using model-based phylogenetic methods, it is possible to test the fit between tree, model and data (step 10 of the new protocol). A suitable test of goodness-of fit was proposed in 1993 (172) (Fig. 4) . In brief, using the inferred optimal tree, including the edge lengths, it is possible to simulate data sets under the null model (i.e., the inferred optimal model of sequence evolution with its parameter values included). This is called a parametric bootstrap. Given this tree and this model of sequence evolution, several sequence-generating programs (5,160,173-175) facilitate procurement of pseudo-data.
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